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Published July 19, 2024 | Version 1.0.0
Software Open

Imageomics/pybioclip: Initial Release

Authors/Creators

  • 1. Center for Genomic and Computational Biology (GCB), Duke University
  • 2. ROR icon The Ohio State University

Description

Command line tool and python package to simplify using BioCLIP.

What's Changed

  • Add bioclip command line tool by @johnbradley in https://github.com/Imageomics/pybioclip/pull/3
  • Improve performance and prediction results by @johnbradley in https://github.com/Imageomics/pybioclip/pull/8
  • Add device parameter and examples by @johnbradley in https://github.com/Imageomics/pybioclip/pull/9
  • Add embed command by @johnbradley in https://github.com/Imageomics/pybioclip/pull/10
  • Fix for RGBA png files by @johnbradley in https://github.com/Imageomics/pybioclip/pull/13
  • Avoid recomputing text embeddings for custom labels by @johnbradley in https://github.com/Imageomics/pybioclip/pull/16
  • Allow batch processing of images by @johnbradley in https://github.com/Imageomics/pybioclip/pull/18
  • Prep to release on pypi by @johnbradley in https://github.com/Imageomics/pybioclip/pull/19
  • Fixes badges to use the correct package name by @hlapp in https://github.com/Imageomics/pybioclip/pull/21

Full Changelog: https://github.com/Imageomics/pybioclip/commits/1.0.0

Files

Imageomics/pybioclip-1.0.0.zip

Files (2.1 MB)

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Additional details

Related works

Is supplement to
Software: https://github.com/Imageomics/pybioclip/tree/1.0.0 (URL)

Funding

U.S. National Science Foundation
HDR Institute: Imageomics: A New Frontier of Biological Information Powered by Knowledge-Guided Machine Learning 2118240

References

  • Stevens S, Wu J, Thompson MJ, Campolongo EG, Song CH, Carlyn DE, Dong L, Dahdul WM, Stewart C, Berger-Wolf T, Chao W-L, Su Y (2024) BioCLIP: A Vision Foundation Model for the Tree of Life. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), 19412–19424.